[gmx-users] amidated C-terminal residue of peptide

[Justin Lemkul]

On 5/27/16 8:25 AM, kamakshi sikka wrote:
> Hello all,
>
> I am doing  membrane peptide simulation studies using POPS/POPC membrane
> built by Charmm GUI. While generating the topology file for the amidated
> peptide, I get a fatal error:                '*Residue 'NHE' not found in
> residue topology database'*. I am using Charmm36 force field here. Can you
> please help me in solving this issue.
>

Let CHARMM-GUI build everything for you.  It writes GROMACS topology and input 
files.  There's no need to take anything back into pdb2gmx.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================